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Fixing a bad skull strip

As you can see, the skull strip for this subject is very poor for both timepoints MR1 and MR2, therefore affecting the results of the base and the longitudinals downstream.

If you look at the coronal slice 158 for OAS2_0004_MR1_before, you can see that the entire neck is still present.

If you scroll down to slice 45, you can see that part of the right hemisphere is missing, but is present in T1.mgz.

The same happened to OAS2_0004_MR2_before. At slice 170, a large part of the brain is missing while the neck is still present.

The best way to fix a problem like this is to adjust the watershed parameters. This can only be done on the cross-sectionals, and you'll have to use the edited cross-sectionals to recreate the base and the longitudinals afterwards.

First, adjust the watershed parameters for both MR1 and MR2 using the following commands:

recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR1_before
recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR2_before

Take a look at your output volume (brainmask.mgz has been changed) along with the original T1 volume (T1.mgz), and verify the result of the new skull stripping is correct.

tkmedit OAS2_0004_MR1_before brainmask.mgz -aux T1.mgz -surfs
tkmedit OAS2_0004_MR2_before brainmask.mgz -aux T1.mgz -surfs

The output for both should look like this:

<insert pictures>

After you are satisfied with the results, remember to run the rest of the cross sectional recon-all steps for all timepoints that you made an adjustment to:

recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR1_before
recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR2_before

To save time, you can check in with the recon-all-status.log in the scripts directory of these subjects to see if the normalization step is complete. Once that step is complete, you can start recreating your base.

recon-all -base OAS2_0004 -tp OAS2_0004_MR1_before -tp OAS2_0004_MR2_before -all

Then, the final step is to recreate the longitudinals once base and cross sectional runs are complete.

recon-all -long OAS2_0004_MR1_before OAS2_0004 -all
recon-all -long OAS2_0004_MR2_before OAS2_0004 -all

**NOTE: When recreating the base and longitudinals, it is recommended to remove or rename the existing base and longitudinal directories and start those processes from scratch.

You can examine the corrected version of the base and longitudinals by using the following commands in separate terminals.

tkmedit OAS2_0004 brainmask.mgz -aux T1.mgz -surfs
tkmedit OAS2_0004_MR1.long.OAS2_0004 brainmask.mgz -aux T1.mgz -surfs
tkmedit OAS2_0004_MR2.long.OAS2_0004 brainmask.mgz -aux T1.mgz -surfs

This is only one example of a specific skull strip error, for more details on this type of error, take a look here.